I'm shooting a 5d mark ii right now with a 50L. I rarely shoot over 400iso and am mostly shooting portraits. However, my shots are almost always out of focus. Not from Motion blur. I was wondering if anyone knew how much more accurate the 1ds mark ii's focusing system is compared to the 5d's. I don't do video or anything either. So loosing that isn't an issue.

1DsII definitely has a lot better AF. At the same time keep in mind that 50L also has a reputation of suffering from focus shift which could be a cause of your issues. I haven't used this lens myself so I don't know how real that problem is in practice, but if it is the cause of your issues then it might not be solved by having a better camera

It's curious to me that I have both an ancient 1D2n and 1Ds2, and with all of my lenses, (about a dozen or so), each lens focuses just about perfectly, just about every time. I had a 50D for a while, as well as a 1D3, and had nothing but aggravation with focusing issues (all the same glass) and trying to correct with MA. Wish I could say why this is true, but I know I'm not the only one. Some lenses have been calibrated by Canon service, others not.